PKBDS1737HONR
{
"@context": "/terms/",
"@id": "/analysis-sets/PKBDS1737HONR/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "PKBDS1737HONR",
"aliases": [
"prodo:Prodo_scRNAseq_HP-22234-01__18_hr_NMMA_18_hr_NMMA"
],
"assay_titles": [
"scRNA-seq"
],
"audit": {
"ERROR": [
{
"category": "unexpected input file set",
"detail": "Analysis set [PKBDS1737HONR](/analysis-sets/PKBDS1737HONR/) links to file set(s): [PKBDS9944WWQC](/measurement-sets/PKBDS9944WWQC/) in `input_file_sets` that are not represented in the `derived_from` of the file sets of the files in this analysis. The analysis set input files are expected to belong to the input file sets.",
"level": 60,
"level_name": "ERROR",
"name": "audit_input_file_sets_derived_from",
"path": "/analysis-sets/PKBDS1737HONR/"
}
],
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released treatment [3eaa06df-d9f3-4539-9424-7e7e76ff7e2b](/treatments/3eaa06df-d9f3-4539-9424-7e7e76ff7e2b/) has deleted subobject award [U24DK13851](/awards/U24DK13851/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/treatments/3eaa06df-d9f3-4539-9424-7e7e76ff7e2b/"
}
],
"WARNING": [
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 2 field `rrid`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 2 field `glucose_loweing_theraphy`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 2 field `hospital_stay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 2 field `donation_type`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `dbxrefs`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `phenotypic_features`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `family_history_of_diabetes`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `family_history_of_diabetes_relationship`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `genetic_ethnicities`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `biological_sex`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `diabetes_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `c_peptide`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `aab_gada`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `aab_gada_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `aab_gada_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `aab_ia2`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `aab_ia2_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `aab_ia2_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `aab_iaa`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `aab_iaa_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `aab_iaa_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `aab_znt8`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `aab_znt8_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `aab_znt8_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `hla_typing`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `other_theraphy`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `publication_identifiers`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `documents`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `t1d_stage`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `related_donors`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM8521GSYZ](/primary-islet/PKBSM8521GSYZ/) is missing tier 2 field `rrid`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM8521GSYZ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM8521GSYZ](/primary-islet/PKBSM8521GSYZ/) is missing tier 2 field `organ_source`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM8521GSYZ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM8521GSYZ](/primary-islet/PKBSM8521GSYZ/) is missing tier 2 field `prep_viability`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM8521GSYZ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM8521GSYZ](/primary-islet/PKBSM8521GSYZ/) is missing tier 2 field `warm_ischaemia_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM8521GSYZ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM8521GSYZ](/primary-islet/PKBSM8521GSYZ/) is missing tier 2 field `purity`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM8521GSYZ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM8521GSYZ](/primary-islet/PKBSM8521GSYZ/) is missing tier 2 field `hand_picked`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM8521GSYZ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM8521GSYZ](/primary-islet/PKBSM8521GSYZ/) is missing tier 2 field `pre_shipment_culture_time`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM8521GSYZ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM8521GSYZ](/primary-islet/PKBSM8521GSYZ/) is missing tier 2 field `islet_function_available`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM8521GSYZ/"
},
{
"category": "missing derived from",
"detail": "Analysis set [PKBDS1737HONR](/analysis-sets/PKBDS1737HONR/) links to file(s) [PKBFI7634UZNI](/alignment-files/PKBFI7634UZNI/), [PKBFI9679JWSR](/matrix-files/PKBFI9679JWSR/), [PKBFI5555XYAL](/tabular-files/PKBFI5555XYAL/), [PKBFI6812FWZV](/tabular-files/PKBFI6812FWZV/), [PKBFI9332NOFM](/tabular-files/PKBFI9332NOFM/), [PKBFI2730ACGT](/matrix-files/PKBFI2730ACGT/), [PKBFI8677DQHL](/matrix-files/PKBFI8677DQHL/), [PKBFI5101QGDH](/matrix-files/PKBFI5101QGDH/), [PKBFI3168SIYT](/matrix-files/PKBFI3168SIYT/), [PKBFI2246ZORQ](/matrix-files/PKBFI2246ZORQ/), [PKBFI9476NBFY](/matrix-files/PKBFI9476NBFY/), [PKBFI6846QQIH](/matrix-files/PKBFI6846QQIH/) that have no `derived_from`. Files in an analysis set are expected to be derived from other files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_sets_derived_from",
"path": "/analysis-sets/PKBDS1737HONR/"
}
]
},
"award": {
"@id": "/awards/PSEUDO2/",
"contact_pi": {
"@id": "/users/29948efc-654e-4448-ade8-2fe2cd0a8d4b/",
"title": "Prodo Laboratories"
},
"title": "Prodo Laboratories Inc."
},
"collections": [
"Prodo"
],
"control_for": [],
"creation_timestamp": "2025-05-08T23:24:26.865812+00:00",
"description": "Analysis set of scRNA-seq for islet biosample of human donor HP-22234-01 from Prodo with 18_hr_NMMA (HP-22234-01__18_hr_NMMA)",
"donors": [
{
"@id": "/human-donors/PKBDO5181VXNQ/",
"accession": "PKBDO5181VXNQ",
"aliases": [
"prodo:HP-22234-01"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/alignment-files/PKBFI4712CLQM/",
"accession": "PKBFI4712CLQM",
"aliases": [
"prodo:Prodo_scRNAseq_HP-22234-01__18_hr_NMMA_18_hr_NMMA_Alignment_before-dedup.bam"
],
"content_type": "alignments",
"creation_timestamp": "2025-05-16T16:57:55.433213+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI4712CLQM/@@download/PKBFI4712CLQM.bam"
},
{
"@id": "/alignment-files/PKBFI7634UZNI/",
"accession": "PKBFI7634UZNI",
"aliases": [
"prodo:Prodo_scRNAseq_HP-22234-01__18_hr_NMMA_18_hr_NMMA_Alignment_Aligned.sortedByCoord.out.bam"
],
"content_type": "alignments",
"creation_timestamp": "2025-05-15T23:56:19.528146+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI7634UZNI/@@download/PKBFI7634UZNI.bam"
},
{
"@id": "/matrix-files/PKBFI9679JWSR/",
"accession": "PKBFI9679JWSR",
"aliases": [
"prodo:Prodo_scRNAseq_HP-22234-01__18_hr_NMMA_18_hr_NMMA_Matrix_matrix.mtx"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T16:44:14.251533+00:00",
"file_format": "mtx",
"href": "/matrix-files/PKBFI9679JWSR/@@download/PKBFI9679JWSR.mtx"
},
{
"@id": "/tabular-files/PKBFI5555XYAL/",
"accession": "PKBFI5555XYAL",
"aliases": [
"prodo:Prodo_scRNAseq_HP-22234-01__18_hr_NMMA_18_hr_NMMA_Tabular_Log.final.out"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-15T23:33:12.180871+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI5555XYAL/@@download/PKBFI5555XYAL.txt.gz"
},
{
"@id": "/tabular-files/PKBFI6812FWZV/",
"accession": "PKBFI6812FWZV",
"aliases": [
"prodo:Prodo_scRNAseq_HP-22234-01__18_hr_NMMA_18_hr_NMMA_Tabular_Log.out"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-15T23:38:02.738465+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI6812FWZV/@@download/PKBFI6812FWZV.txt.gz"
},
{
"@id": "/tabular-files/PKBFI9332NOFM/",
"accession": "PKBFI9332NOFM",
"aliases": [
"prodo:Prodo_scRNAseq_HP-22234-01__18_hr_NMMA_18_hr_NMMA_Tabular_Log.progress.out"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-15T23:43:18.146266+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI9332NOFM/@@download/PKBFI9332NOFM.txt.gz"
},
{
"@id": "/matrix-files/PKBFI2730ACGT/",
"accession": "PKBFI2730ACGT",
"aliases": [
"prodo:Prodo_scRNAseq_HP-22234-01__18_hr_NMMA_18_hr_NMMA_Matrix_cellbender_FPR_0.05.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T19:08:58.581052+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI2730ACGT/@@download/PKBFI2730ACGT.h5ad"
},
{
"@id": "/tabular-files/PKBFI7634UOEE/",
"accession": "PKBFI7634UOEE",
"aliases": [
"prodo:Prodo_scRNAseq_HP-22234-01__18_hr_NMMA_18_hr_NMMA_Tabular_qc.txt"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T17:21:52.736856+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI7634UOEE/@@download/PKBFI7634UOEE.txt.gz"
},
{
"@id": "/matrix-files/PKBFI8677DQHL/",
"accession": "PKBFI8677DQHL",
"aliases": [
"prodo:Prodo_scRNAseq_HP-22234-01__18_hr_NMMA_18_hr_NMMA_Matrix_cellbender_FPR_0.05_filtered.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T19:16:58.822483+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI8677DQHL/@@download/PKBFI8677DQHL.h5ad"
},
{
"@id": "/tabular-files/PKBFI8197BODF/",
"accession": "PKBFI8197BODF",
"aliases": [
"prodo:Prodo_scRNAseq_HP-22234-01__18_hr_NMMA_18_hr_NMMA_Tabular_knee.txt"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T17:26:59.481840+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI8197BODF/@@download/PKBFI8197BODF.txt.gz"
},
{
"@id": "/tabular-files/PKBFI5910FCDD/",
"accession": "PKBFI5910FCDD",
"aliases": [
"prodo:Prodo_scRNAseq_HP-22234-01__18_hr_NMMA_18_hr_NMMA_Tabular_pass.txt"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T17:38:25.868691+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI5910FCDD/@@download/PKBFI5910FCDD.txt.gz"
},
{
"@id": "/tabular-files/PKBFI3811XIIN/",
"accession": "PKBFI3811XIIN",
"aliases": [
"prodo:Prodo_scRNAseq_HP-22234-01__18_hr_NMMA_18_hr_NMMA_Tabular_cellbender_FPR_0.05_metrics.csv"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T18:45:40.868190+00:00",
"file_format": "csv",
"href": "/tabular-files/PKBFI3811XIIN/@@download/PKBFI3811XIIN.csv.gz"
},
{
"@id": "/tabular-files/PKBFI1308LKKY/",
"accession": "PKBFI1308LKKY",
"aliases": [
"prodo:Prodo_scRNAseq_HP-22234-01__18_hr_NMMA_18_hr_NMMA_Tabular_cellbender_cell_barcodes.csv"
],
"content_type": "sequence barcodes",
"creation_timestamp": "2025-05-16T17:45:40.469758+00:00",
"file_format": "csv",
"href": "/tabular-files/PKBFI1308LKKY/@@download/PKBFI1308LKKY.csv.gz"
},
{
"@id": "/tabular-files/PKBFI1619TQRL/",
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Supported by National Institutes of Health (NIH) grants U24 DK138515, U24 DK138512
Supplemental funds from the NIH Office of Data Science Strategies
Supplemental funds from the NIH Office of Data Science Strategies